Question: Best way to filter a list of diseases by those relating to the immune system?
0
gravatar for psyc_biostars
4 months ago by
psyc_biostars0 wrote:

I have a list of diseases which I got from GWAS Catalog associations. However, I want to be able to filter these out systematically (via R), leaving only diseases related to the immune system.

Does anyone have any suggestions for how to do this? I thought it might be an idea to get a list of all immune diseases and all immune cell types, and to keep any entry that mentions those terms.

R • 152 views
ADD COMMENTlink modified 4 months ago by Pierre Lindenbaum131k • written 4 months ago by psyc_biostars0

Please add more relevant tags. Is R really the only relevant tag here?

ADD REPLYlink written 4 months ago by RamRS30k
2
gravatar for Pierre Lindenbaum
4 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

GWAS use the Experimental Factor Ontology https://www.ebi.ac.uk/ols/ontologies/efo . There is an associated OWL file for download . I've got a tool that performs a very basic scan over all the simple children of a given term. For immune system disease I get the following terms that you can use to 'grep' the database.

ADD COMMENTlink written 4 months ago by Pierre Lindenbaum131k

Great resource, thank you - what is the tool that you use to do this?

ADD REPLYlink written 4 months ago by psyc_biostars0
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